Journal of Environment and Sociobiology

Sankar Kumar Ghosh ¹, Prabal Ranjan Ghosh ², Tarikul Huda Mazumder ¹, Miranda Kshetrimayum ¹

Affiliations
1 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN
2 Department of Vetarinary Physiology, WBUAFS, Kolkata-700 037, W.B., IN

Abstract

Northeast India is a reservoir of rich biodiversity, especially Greater one-horned rhinoceros (Rhinoceros unicornis) which is facing extinction. DNA barcoding being an exciting tool for accurate documention of biodiversity with a gene sequence, in the present article DNA barcode of R. unicornis is determined for the first time by amplifying mitochondrial COI gene region using cross species primer designing and other bioinformatics analysis (Accession No. JN41700). Phylogeny analysis of obtained sequence with other related species distinctly maintains the assigned taxonomic position.

Keywords

DNA Barcoding, Mitochondrial DNA, COI-5', Rhinoceros Unicornis

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Prabal Ranjan Ghosh ¹, Pradosh Mahadani ², Rosy Mondal ², Pradip Kumar Das ¹, Sankar Kumar Ghosh ²

Affiliations
1 West Bengal University of Animal and Fishery Sciences, Kolkata-700037, West Bengal, IN
2 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

Poultry biodiversity widely prevails over the world, especially in Indian subcontinent as domestic indigenous fowl. Cross species hybridization of different Gallus species confers ambiguity in proper classification. Molecular approach using DNA barcoding to identify species boundaries is successfully employed to detect hybridization signal of nondescript indigenous fowls. In the present study DNA barcoding region of cytochrome oxidase I (COI) gene collected from geographically distant region of five agroclimatic zones of eastern India is amplified using PCR, sequenced and subsequently deposited in GenBank. Related sequences were retrieved from global databases for phylogenic analysis using bioinformatics. The present study provides for the first time the DNA barcodes of domestic fowls from eastern India and established that the domestic fowls are grouped within the group Gallus gallus. Additional COI sequences within the same and related genus collected from different countries properly discriminate and assign their correct taxonomic positions. Low level of interspecies variation was observed between Gallus gallus and Gallus sonneratii indicating the failure to discriminate them as separate species.

Keywords

DNA Barcoding, Poultry, Gallus Gallus, MtDNA, Cytochrome Oxidase I, Genbank.

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Prabal Ranjan Ghosh ¹, Monika Ahanthem ², Pradosh Mahadani ², Amalesh Choudhury ³, Sankar Kumar Ghosh ²

Affiliations
1 West Bengal University of Animal and Fishery Sciences, Kolkata-700037, West Bengal, IN
2 Department of Biotechnology, Assam University, Silchar-788011, IN
3 S. D. Marine Institute, Sunderban, West Bengal, IN

Abstract

Chicken domestication plays an important role for major supply of animal protein throughout the world. In India, wide diversities of domestic chicken are descended from wild red jungle fowl (RJF) (Gallus gallus), the mother of all fowls of the world. In the present study, DNA barcode sequence and cytochrome c oxidase subunit I (COI) region of wild RJF from northeastern India using PCR are determined, sequenced and subsequently deposited in GenBank (Accession No. JN793568). The study provides for the first time the DNA barcodes of red jungle fowl from northeastern India and subsequent bioinformatics yield that the RJF is grouped within correct taxonomic assignment of other Gallus species proving strong resolving power of DNA barcode in chicken.

Keywords

Cytochrome C Oxidase Subunit I, DNA Barcodes, Red Jungle Fowl, Gallus gallus, Northeastern India.

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Shantanu Kundu ¹, Kulendra Chandra Das ¹, Sankar Kumar Ghosh ¹

Affiliations
1 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

The purpose of DNA barcodes for the rapid and accurate identification of wild species is one of the satisfactory and promising applications in forensic sciences. Here we developed eight 598 by sequences of COI (cytochrome c oxidase subunit I) locus for the accurate identification of commercialized turtle samples collected from different markets of East and Northeast India.The studied samples were successfully identified as two subspecies of Lissemys punctata, namely, L. p. andersoni and L. p. punctata with their limited morphometric data and sequence allignment results (99%-100% with L. punctata) in both BLASTn and BOLD IDs. Further, the studied sequences revealed less nucleotide (1.5%) and amino acid (0.5%) variationas as well as minimal K2P divergence (0% - 1.5%) in both L. p. andersoni and L. p. punctata. Partial barcode sequences are not efficient to delineate the subspecies of L. punctata. This study validated that the use of partial COI marker could overcome the lack of mophometric data to achieve higher accuracy detection of any commercialized as well as forensic samples.

Keywords

Chelonians, Trionychids, Cytochrome Oxidase C Subunit I (COI), Subspecies, Forensic, Conservation.

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Shantanu Kundu ¹, Kulendra Chandra Das ¹, Sankar Kumar Ghosh ¹

Affiliations
1 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

Limited molecular examinations are sometimes difficult to differentiate 31 morphologically distinct Indian testudine species. Mitochondrial genes have recurrently been used as molecular markers in various productive evolutionary studies. The total 73 available barcode sequences (621bp) of testudine species were acquired from public database. The total nucleotide variation was found to be 293 positions but the amino acid variation was found in only 57 positions among the all turtle and tortoise species. The first codon position in Indian testudines was more GC bias (54%) compared to the other second and third codon position. The highest substitutions were found in Non polar group (0.03% - 16.17%) compared to the other groups, by checking their different codon positions. The minimum amino acids informative sites within the COI barcode sequences may be practicable for discriminating all Indian testudine species.

Keywords

Chelonians, Cytochrome Oxidase C Subunit I (COI), Amino Acid, Substitution.

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Bijoya Khomdram Devi ¹, Bishal Dhar ¹, Boni Amin Laskar ¹, Sankar Kumar Ghosh ²

Affiliations
1 DNA barcode and Genomics Laboratory, Department of Biotechnology, Assam University, Silchar-788011, Assam, IN
2 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

DNA barcoding is an effective technique of species identification. The large reference library of DNA barcode should be enriched from every region and may be assessed together with morphological taxonomy for species authentication. In this study, a total of 27 fish samples belonging to 21 different species having ornamental relevance were collected and morphologically identified from Manipur, Northeast India. DNA was isolated from muscle tissue of samples and then COI barcode region was amplified using universal fish primers, sequenced and submitted to NCBI (Accession nos. JQ713844 - JQ713860). The sample sequences were identified through similarity search in two databases : GenBank and BOLD. Both the databases revealed definitive identity matches in the range of 98.37% - 100% for 44% of the species. This indicated that the database still lacks reference data of ornamental fishes of Manipur and this study contributed new barcode sequences of ornamental fishes.

Keywords

Ornamental Fish, Manipur, DNA Barcoding, COI, Sequence Homology.

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Miranda Kshetrimayum ¹, Sankar Kumar Ghosh ², Monika Ahanthem ¹

Affiliations
1 DNA barcode and Genomics Laboratory, Department of Biotechnology, Assam University, Silchar-788011, Assam, IN
2 Department of Biotechnology, Assam University, Silchar-788011, Assam, IN

Abstract

Identification of forensic articles like carcasses or marketed products is difficult. Although recent molecular advancement provides use of fragments of cytochrome c oxidase I (COI) as species level marker in all animals, yet primers are diverse among groups of animals. So, primer selection for any unstructured specimen is difficult. We explored possibility of cross species primer to amplify the DNA barcode fragment of COI for a native horse species (Equus caballus). Different barcode primers of common taxa are empirically tested in silico. Based on the critical criteria of DNA barcoding resultantly forward primer for Bird DNA barcoding and reverse primer for Fish DNA gave an in silico PCR product of 699 bp, also verified in vitro using genomic DNA extracted from hair samples. The sequence similarity and homology search in BOLD nucleotide database confirm specific identification. This study forecasts application of cross species primer to identify suspected biological sample in diverse arena.

Keywords

Forensic Science, Cytochrome C Oxidase 1, Cross Species Primer, In Silico, Bold, Unstructured Specimen.

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